The invention discloses a system of treatment by deep cooling with temperature controlling based on natural circulation. The system is composed of liquid nitrogen tank, filling port, perfusion valve, perfusion tube, heat insulating layer, cold shield, treatment room for deep cooling, internal coil, external coil, pressure transducer of internal-coil entry, temperature transducer of internal-coil entry, fan, nitrogen cylinder, reducing valve, injection control valve, injection tube, pressure transducer of external-coil entry, temperature transducer of external-coil entry, temperature transducer in treatment room for deep cooling, reflux control valve, reflux tube, data acquisition of computer and control system. The system depends on pressure-difference resulting from different consistency of liquid nitrogen and gas nitrogen to impel coolant of liquid nitrogen for circular flowing. Adjusting of coefficient of heat transfer on the surface of work is realized conveniently by controlling flux of circulate liquid nitrogen and rotate speed of fan. The system has much strongpoint including saving circulate power and consumption of liquid nitrogen, easy to control cooling speed of treatment by deep cooling and treatment temperature etc.